Curriculum Vitae

Biodiversity Informatician

Summary

Web Application Developer in a variety of biodiversity informatics applications. Particularly interested in data transformations and social interaction using generic open source tools. I combine a strong background in traditional alpha taxonomy and modern molecular techniques with a good understanding of the current state of the art in biodiversity informatics and familiarity with a whole suite of software tools and programming languages.

Contact Details

Name Kehan Tristam Harman Born 16 May 1977, Mbabane, Swaziland, Africa
Address 63 Balvernie Grove, Southfields, London, SW18 5RR, UK
Phone +44 (0)20 8874 9229 Mobile +44 (0)78 5938 4584
email kehanharman@gmail.com skype kehanharman

Qualifcations

M.Sc. in Bioinformatics (77%). 2005-2007 (Part time course): Modules included Perl & Java Programming, Bioinformatics Algorithms & Tools, Statistics, Database Management (MySQL & Oracle). Group project in software engineering. Research project: GrassBase – Steps toward integrating the Online World Grass Flora. Involved developing a prototype Drupal based Grass portal for the integration of Kew’s grass databases. Cranfield University, UK.
B.Sc.Hons in Botany (73%). 2000: Modules: Advanced Systematics, African Phytogeography, Molecular Ecology and Climate Change. Rhodes University, Grahamstown, South Africa.
B.Sc. in Botany (77.5%) and Microbiology (70.5%). 1997-1999: Rhodes University, Grahamstown, South Africa.
I.B. International Baccalaureate Diploma. 1994-1995: Higher Level: Biology (6), Chemistry(5) and Mathematics (5); Subsidiary Level: English Literature (4), French (5) and Geography (5) Waterford Kamhlaba, United World College of Southern Africa, Mbabane, Swaziland.
O-Level University of Cambridge O Level Certificate. 1992-1993: Nine O-Levels with an aggregate 13 Points. Waterford Kamhlaba, United World College of Southern Africa, Mbabane, Swaziland

Bioinformatics Skills

Programming – in PHP, Perl, Java, MATLAB and Visual Basic (VB)/VBA. PHP extensively used in Drupal module development. Visual Basic used in maintaining Kew’s grass databases including VB programs to manipulate DELTA text files and work on the user interface of the MS Access synonymy database. Java used in developing a web based reference management tool as part of a group project. Additionally some work using the AppFuse2 Java Application Development framework based on Maven, Struts and Hibernate. Perl used for text (including DNA sequence) manipulation & database connectivity.

Database Administration – Advanced MySQL and MS Access, intermediate SQLite and basic Oracle and PostgreSQL.

Drupal – Extensive knowledge of the Drupal open source content management framework including site building and administration, available modules, module development and participation in its open source development community. Knowledge of Drupal concepts including Hooks, Nodes, Taxonomy, Views and CCK.

Team based software development – using both Eclipse and NetBeans IDE, using SVN, CVS and GIT version control systems, with project management and issue tracking using Sourceforge, Google Code, Trac, Drupal.org and Launchpad. Use of Wiki’s including MediaWiki and TWiki for team collaboration.

TDWG Standards – Extensive experience of DELTA, TDWG content standards (geography and literature), knowledge of SDD, TCS, ABCD/DarwinCore including the TDWG Ontology. Knowledge of the OGC (Open Geospatial Consortium) standards and how they relate to biodiversity data.

Traditional bioinformatics – Knowledge of a suite of software tools currently used. Working on various data types including output from microarray, mass spectrometry and gas chromatography experiments, the large molecular databases such as GenBank, Ensembl, Uniprot and PDB. Statistical analysis including cluster analysis, PCA and machine learning using both R and Matlab, sequence manipulation using Perl and Java.

General computer skills – Touch typing (75 WPM), Word Processing, Spreadsheet, Database and Email in all versions of Linux, Windows and Mac OS X operating systems. System administration with extensive experience administrating Ubuntu Linux servers including software updates, backup regimes, Apache Web Server, shell scripting, mail handling and user management. Computer building, systems administration, networking and troubleshooting.

Scientific Skills

Molecular Biology – PCR, DNA extraction, manipulation, sequencing and fingerprinting. Cell culture, cloning, virology.

Microscopy – Light (Dissecting and Compound), Scanning and Transmission Electron Microscopy.

Molecular Ecology and Systematics – Fieldwork, data capture and analysis in these disciplines including population genetics, phylogenetic analysis and morphometrics.

Grass morphology and taxonomy – preparation of species descriptions in DELTA format, identification of grasses using traditional and interactive keys. Herbarium specimen preparation, curation and identification.

Communication

Verbal – Experience as a game ranger, salesperson and a tutor, work in various committees and presentation of seminars. Written – several publications, two Honours theses, posters presented at three international conferences, report writing and numerous essays. Presentation – Individual and group presentations at numerous international conferences and symposia. Selected to represent the Monocot section at Kew during a recent science audit.

Teamwork

Member of the Global Checklist Steering Group, Royal Botanic Gardens, Kew. 2006-2007; Working as a Game Ranger involved close teamwork with my personal tracker and with other rangers over the radio in order to maximise game viewing for guests.

Relevant Experience

Researcher, GBIF Funded – The Natural History Museum, London. Mar 2008 – Present: Software development to support the GBIF ECAT programme. Using the Scratchpads (http://scratchpads.eu) framework (based on Drupal) to develop various community interaction tools including the GBIF vocabularies and extension server (http://vocabularies.gbif.org). This involves using my taxonomic and computing background to develop a suite of Drupal modules.

Database and Collections Officer – Royal Botanic Gardens, Kew, London. Feb 2005 – Jan 2008: Managing and developing Kew’s grass synonymy and DELTA descriptive databases, and helping to make them web accessible (see bioinformatics skills above). Curation and identification of grass and other Monocot specimens for the global collection. Included developing a prototype web portal for my M.Sc. research project. Standardising nomenclature database according to TDWG content standards.

Global Checklist Project Officer – Royal Botanic Gardens, Kew, London. May 2004 – Jan 2005: Digitisation and georeferencing of herbarium specimens, preparation of preliminary conservation assessments and data analysis. Contributed to final report for the iPlants (http://iplants.org) pilot project.

Game Ranger – Mala Mala Game Reserve, Kruger Park, South Africa. Jan – Sep 2001: A dual role involving conservation and natural resource management combined with hosting international guests at a 5 star private game reserve both in camp and as a guide on game drives throughout the day.

Student Intern – Molecular Ecology Unit, Institute of Terrestrial Ecology at Furzebrook, Dorset. Nov 1999 – Feb 2000: Carried out a research project DNA fingerprinting a South African plant population in a Molecular Ecology Laboratory.

Reference Database Management and Report Writing – Rhodes University, South Africa. July 1998 – July 1999: Worked for various academic staff setting up and maintaining a number of databases of scientific literature, and the compilation of a number of separate research articles into a final research report.

Academic Achievements

2000: Lillian Britten Prize for Botany III. Awarded to the top student.

2000: NRF (National Research Foundation) Freestanding Scholarship and Rhodes University Honours Degree Scholarship. Awarded for Botany Honours on the basis of my performance during my B.Sc. Degree.

1998 & 2000: Academic Half Colours, Rhodes University. Two merit awards based on academic performance in my first and final years of my B.Sc. Degree.

Interests and Hobbies

Rock-climbing including an Outstanding Service Award for the Rhodes University Mountain club, Hiking, Mountain Biking and Yacht & Dinghy Sailing. Plant and Wildlife Conservation, photography, computer building, programming and operation.

Publications

Smith, VS, Rycroft, SD, Harman, KT, Scott, B, Roberts, DMcL. (In Press). Scratchpads: a data-publishing framework to build, share and manage information on the diversity of life. BMC Bioinformatics.

Roberts, D, Rycroft, SD, Brake, I, Harman, K, Scott, B, Smith, VS. (2008). Getting Taxonomy onto the Web. The Systematist 30: 3.

Mayo, SJ, Allkin, R, Baker, W, Blagoderov, V, Brake, I, Clark, B, Govaerts, R, Godfray, C, Haigh, A, Hand, R, Harman, K, Jackson, M, Kilian, N, Kirkup, DW, Kitching, I, Knapp, S, Lewis, GP, Malcolm, P, von Raab-Straube, E, Roberts, DM, Scoble, M, Simpson, DA, Smith, C, Smith, VS, Villalba, S, Walley, L, Wilkin, P. (2008). Alpha e-taxonomy: responses from the systematics community to the biodiversity crisis. Kew Bulletin 63: 1-16. DOI: 10.1007/s12225-008-9014-1.

Paton, AJ, Brummitt, N, Govaerts, R, Harman, K, Hinchcliffe, S, Allkin, R, Nic Lughadha, E. (2008). Towards Target 1 of the Global Strategy for Plant Conservation: a working list of all known plant species—progress and prospects. Taxon 57(2): 602-611.

Harman, KT, Clayton, WD. (2007). Recent developments in Kew’s grass databases (GrassBase). Kew Bulletin 62: 375-379.

Clayton, WD, Harman, KT & Williamson, H. (2006 onwards). World Grass Species: Descriptions, Identification, and Information Retrieval. Published online: http://www.kew.org/data/grasses-db/.

Clayton, WD, Harman, KT & Williamson, H. (2006 onwards). World Grass Species: Synonymy. Published online: http://www.kew.org/data/grasses-syn/.

Wilkins, KJ, Harman, KT & Villet, MH. (2006). Recruitment behaviour in the ponerine ant, Plectroctena mandibularis F. Smith (Hymenoptera: Formicidae). African Entomology 14(2): 367-372.

Barker, NP, Harman, KT, Ripley, BS, Bond, J. (2002). The genetic diversity of Scaevola plumieri (Goodeniaceae), an indigenous dune coloniser, as revealed by Inter Simple Sequence Repeat (ISSR) Fingerprinting. South African Journal of Botany 68: 532-541.

References

David Remsen. ECAT Programme Officer. GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark. Coordinator of my current work programme and remote line manager. dremsen@gbif.org +45 2875 1472

Dr David McL. Roberts. Researcher. Dept. of Zoology, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK. Head of the research group that I’m working in and is coordinator for the EDIT (European Distributed Institute for Taxonomy) Workpackage 6 (Unifying Revisionary Taxonomy). dmr@nomencurator.org +44 2079 425086

Dr David Simpson, Assistant Keeper for Monocots. Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK. Line Manager in Database and Collections officer Job. d.simpson@kew.org +44 2083 325260

Dr Conrad Bessant, Senior Lecturer in Chemometrics & Bioinformatics. Cranfield Health, Cranfield University, Silsoe, Bedfordshire MK45 4DT, UK. M.Sc.Supervisor & Course Coordinator. c.bessant@cranfield.ac.uk +44 1525 863358

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